Here's the issue:

I'm creating a group of creatures that all have...similar features, clockwork [insert name here]. Nobody else has made anything with the specific names I was choosing. One is a clockwork gear mage, and the other a clockwork servitor. Here's the deal: they are different in that one is a more powerful version of the other (the servitor being a CR 12 critter with more spells and more hitpoints, and better stats). When I made the clockwork gear mage, I had an issue with my clockwork guardian and it replacing each other!!! So my guardian would disappear and the gear mage would appear. They have similar abilities (they shared a few abilities, like construct nature, clockwork heart, etc...), but again, had wholly different names, ability scores, HP, and each had additional abilities that differed. I'm not sure how I did it, but eventually they separated.

Note: to make the gear mage, I used the base of the guardian (creating what began as a "COPY_OF_" creation) to create the gear mage, and the gear mage to create the servitor. The problem is that I have no idea what in the world I did that eventually separated them, and am now having a problem "separating" the gear mage from the servitor!

Halp, I needs assistance!

Edit: Each time I try to create a new one based on the old one, it comes up as a "version" of what I saved and published last. Not sure if that helps.

That’s a system fault, it gets “templates” and “new versions” confused on published homebrew monsters. Sucks eggs, I know. Yet another one of the excellent reasons to make sure all your homebrews are 1,000% perfect prior to publishing. 

Gah. Well, I *did* find a workaround, although it didn't make me happy. You just have to build it from scratch. Every. Time. Blech.

Oh, well, I have some typing to do.

Not every time. As long as your monster is unpublished, the templating process will work correctly. It’s the publishing that’s the problem.